fixed trim.seqs group counts by adding back in the primer group

[mothur.git] / readtree.h

diff --git a/readtree.h b/readtree.h
index 15597bafbfd64eb88c2f4304aff0fb9b78ac60ea..7cfb4b426eef1ca38e562ae1c52b4ad240afc4e3 100644 (file)
--- a/readtree.h
+++ b/readtree.h
@@ -9,10 +9,8 @@
  *
  */
 
-using namespace std;
-
+#include "mothur.h"
 #include "globaldata.hpp"
-#include "utilities.hpp"
 #include "tree.h"
 
 #define MAX_LINE               513
@@ -25,7 +23,7 @@ class Tree;
 class ReadTree {
        public:
                ReadTree(); 
-               ~ReadTree() {};
+               virtual ~ReadTree() {};
                
                virtual int read() = 0;
                int readSpecialChar(istream&, char, string);
@@ -35,6 +33,7 @@ class ReadTree {
        protected:
                GlobalData* globaldata;
                int numNodes, numLeaves;
+               MothurOut* m;
                
                
 };
@@ -44,7 +43,7 @@ class ReadTree {
 class ReadNewickTree : public ReadTree {
        
 public:
-       ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); readOk = 0; } 
+       ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; } 
        ~ReadNewickTree() {};
        int read();
        
@@ -52,7 +51,7 @@ private:
        Tree* T;
        int readNewickInt(istream&, int&, Tree*);
        int readTreeString();
-       void nexusTranslation();
+       string nexusTranslation();
        ifstream filehandle;
        string treeFile;
        string holder;